Getting the data in R

Source of 95% problems

Author
Affiliation

Julien Martin

University of Ottawa

Published

April 29, 2024

0.1 Learning outcomes

  • recognise different types of data in R ✔️

  • understand some different data structures ✔️

  • learn how to import data into R ✔️

  • learn how to manipulate data in R ✔️

  • learn how to export data from R ✔️

0.2 types of data in R

six types of data in R

  • numeric - 1.618, 3.14, 2.718

  • integers - 1, 2, 3, 42, 101

  • logical - TRUE or FALSE

  • character - “BI5009”, “Blue”

  • complex

  • raw

0.3 data structures

five data structures

  • vector

  • matrix

  • array

  • data frame

  • list

0.4 vectors

  • one dimensional collection elements

  • can contain all data types

  • all elements must be of the same type

0.5 matrices and arrays

  • a vector with extra dimensions

  • again, objects must be of the same type

  • arrays are multidimensional matrices

mat.1 <- matrix(1:12, nrow=4)
mat.1
     [,1] [,2] [,3]
[1,]    1    5    9
[2,]    2    6   10
[3,]    3    7   11
[4,]    4    8   12

array.1 <- array(1:16, dim=c(2,4,2))

0.6 data frames

  • most commonly used data structure for statistical data analysis

  • powerful 2-dimensional vector holding structure

  • dataframes can hold vectors of any of the basic classes of data

   treat nitrogen block height weight leafarea shootarea flowers
1    tip   medium     1    7.5   7.62     11.7      31.9       1
2    tip   medium     1   10.7  12.14     14.1      46.0      10
3    tip   medium     1   11.2  12.76      7.1      66.7      10
4    tip   medium     1   10.4   8.78     11.9      20.3       1
5    tip   medium     1   10.4  13.58     14.5      26.9       4
6    tip   medium     1    9.8  10.08     12.2      72.7       9
7    tip   medium     1    6.9  10.11     13.2      43.1       7
8    tip   medium     1    9.4  10.28     14.0      28.5       6
9    tip   medium     2   10.4  10.48     10.5      57.8       5
10   tip   medium     2   12.3  13.48     16.1      36.9       8

0.7 tidy data

0.8 importing data

  • simplest method is to use spreadsheet
    and then import data into R

  • save as a comma separated file (*.csv)

0.9 Importing data tips

  • missing data represented with NA or empty cells. Do not mixed both

  • No spaces in names (use underscore if needed)

  • no uppercase

  • keep variable names short & informative

0.10 importing data

  • the read.table() function is the workhorse with format specified function to make coding faster
  petunia <- read.table('data/flowers.csv', header = TRUE, sep = ',')


petunia name of the new object
read.table() function use tot read tha data
‘data/flowers.csv’ relative path name to the data file
header = TRUE first line contain columns names
sep = ‘,’ columns sparated by commas

0.11 importing data

  • sometimes columns are separated by tabs, sep = "\t"
petunia <- read.table('data/flowers.csv', header = TRUE, sep = '\t')
  • you can use format specific functions
petunia <- read.csv('flowers.csv')      # if comma-separated 
petunia <- read.delim('flowers.txt')      # if tab-separated

  • functions in the foreign package allows you to import files of other formats (i.e. from SAS, SPSS, Minitab etc)

  • use the readxl or readODS package to directly import MS Excel or LO calc spreadsheets directly

0.12 importing data

  • to view the contents of a data frame, type it’s name

  • rarely a good idea as just fills up your console

  • use the head() and tail() to see first/last 6 lines

[1] flowers
  treat nitrogen block height weight leafarea shootarea flowers
1   tip   medium     1    7.5   7.62     11.7      31.9       1
2   tip   medium     1   10.7  12.14     14.1      46.0      10
3   tip   medium     1   11.2  12.76      7.1      66.7      10
4   tip   medium     1   10.4   8.78     11.9      20.3       1
5   tip   medium     1   10.4  13.58     14.5      26.9       4
6   tip   medium     1    9.8  10.08     12.2      72.7       9

0.13 data wrangling

  • str() function: data frame dimensions, list of variables, type of variables
> str(flowers)
'data.frame':   96 obs. of  8 variables:
 $ treat    : chr  "tip" "tip" "tip" "tip" ...
 $ nitrogen : chr  " medium" " medium" " medium" " medium" ...
 $ block    : int  1 1 1 1 1 1 1 1 2 2 ...
 $ height   : num  7.5 10.7 11.2 10.4 10.4 9.8 6.9 9.4 10.4 12.3 ...
 $ weight   : num  7.62 12.14 12.76 8.78 13.58 ...
 $ leafarea : num  11.7 14.1 7.1 11.9 14.5 12.2 13.2 14 10.5 16.1 ...
 $ shootarea: num  31.9 46 66.7 20.3 26.9 72.7 43.1 28.5 57.8 36.9 ...
 $ flowers  : int  1 10 10 1 4 9 7 6 5 8 ...

0.14 data wrangling

  • names() function: vector of variable names
> names(flowers)
[1] "treat"     "nitrogen"  "block"     "height"    "weight"    "leafarea" 
[7] "shootarea" "flowers"

0.15 data wrangling

  • access variables in your data frame using the $ notation
> flowers$height
 [1]  7.5 10.7 11.2 10.4 10.4  9.8  6.9  9.4 10.4 12.3 10.4 11.0  7.1  6.0  9.0
[16]  4.5 12.6 10.0 10.0  8.5 14.1 10.1  8.5  6.5 11.5  7.7  6.4  8.8  9.2  6.2
[31]  6.3 17.2  8.0  8.0  6.4  7.6  9.7 12.3  9.1  8.9  7.4  3.1  7.9  8.8  8.5
[46]  5.6 11.5  5.8  5.6  5.3  7.5  4.1  3.5  8.5  4.9  2.5  5.4  3.9  5.8  4.5
[61]  8.0  1.8  2.2  3.9  8.5  8.5  6.4  1.2  2.6 10.9  7.2  2.1  4.7  5.0  6.5
[76]  2.6  6.0  9.3  4.6  5.2  3.9  2.3  5.2  2.2  4.5  1.8  3.0  3.7  2.4  5.7
[91]  3.7  3.2  3.9  3.3  5.5  4.4

  • you can extract elements using the [rowIndex, columnIndex] method

  • Index can either be a positional index or a logical index

0.16 positional index

  • provide the row and column position of the data you wish to extract

  • index can either be a positional index or a logical index

flowers[1, 4]      # extract value of first row and 4th column
[1] 7.5
  • extract multiple elements by supplying vectors
flowers[1:3, 1:4]      # extract rows 1 to 3 and columns 1 to 4
  treat nitrogen block height
1   tip   medium     1    7.5
2   tip   medium     1   10.7
3   tip   medium     1   11.2

0.17 positional index

  • another example
1flowers[c(3, 8, 20), c(1, 4, 5, 6)]
1
rows 3, 8 and 20 and columns 1, 4, 5 and 6 
   treat height weight leafarea
3    tip   11.2  12.76      7.1
8    tip    9.4  10.28     14.0
20   tip    8.5  14.33     13.2

  • can assign these extracted values to another object if you want

  • new object inherits data.frame class

flowers_red <- flowers[c(3, 8, 20), c(1, 4, 5, 6)]
flowers_red

0.18 positional index

  • we can use a short cut if we want all rows or all columns extracted

  • omitting the column index is shorthand for ‘all columns’

> flowers[1:3, ]
  treat nitrogen block height weight leafarea shootarea flowers
1   tip   medium     1    7.5   7.62     11.7      31.9       1
2   tip   medium     1   10.7  12.14     14.1      46.0      10
3   tip   medium     1   11.2  12.76      7.1      66.7      10
  • omitting the row index is shorthand for ‘all rows’
> flowers[, 1:3]

0.19 positional index

  • an alternative method to select columns is to name the columns directly for columnIndex
> flowers[1:10, c('treat', 'nitrogen', 'leafarea', 'shootarea')]
   treat nitrogen leafarea shootarea
1    tip   medium     11.7      31.9
2    tip   medium     14.1      46.0
3    tip   medium      7.1      66.7
4    tip   medium     11.9      20.3
5    tip   medium     14.5      26.9
6    tip   medium     12.2      72.7
7    tip   medium     13.2      43.1
8    tip   medium     14.0      28.5
9    tip   medium     10.5      57.8
10   tip   medium     16.1      36.9

0.20 logical index

  • we can also extract rows based on a logical test

  • example, all rows where the height variable is greater than 12

> flowers[flowers$height > 12,]
   treat nitrogen block height weight leafarea shootarea flowers
10   tip   medium     2   12.3  13.48     16.1      36.9       8
17   tip     high     1   12.6  18.66     18.6      54.0       9
21   tip     high     1   14.1  19.12     13.1     113.2      13
32   tip     high     2   17.2  19.20     10.9      89.9      14
38   tip      low     1   12.3  11.27     13.7      28.7       5
  • or where leafarea is equal to 8.7
flowers[flowers$leafarea == 8.7,]

0.21 logical index

  • we can combine logical tests using the & symbol (AND) or the | symbol (OR)

  • example, extract all rows where height is > 10.5 and nitrogen is equal to "medium"

flowers[flowers$height > 10.5 & flowers$nitrogen == 'medium',]
  • or height is greater than 12.3 OR less than 1.8
flowers[flowers$height > 12.3 | flowers$height < 1.8,]

0.22 exporting data frames

  • the write.csv() function exports data frames to an external file


write.csv(flowers, 'flowers2.csv', row.names = FALSE)


  • saves flowers data frame to a file named ‘flowers.csv’

  • row.names = FALSE argument supresses the row names in the file

0.23 other options

  • there are many other options for importing and exporting data in R

  • the fread() and fwrite() functions in the read.table package are blazingly fast

  • the read_csv() and write_csv() (and other related) functions from the readr package for tidyverse alternatives

  • if you have a lot of data (I mean alot!) then take a look at the ff and bigmemory packages

1 Thanks!

Credit: I borrowed slides from Alex Douglas